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29th international conference on dna computing and molecular programming, dna 2023

作者： Berleant, Joseph Don Department of Biological Engineering Massachusetts Institute of Technology CambridgeMA United States

ISBN: (纸本)9783959772976

molecular computation involving promiscuous, or non-orthogonal, binding interactions between system components is found commonly in natural biological systems, as well as some proposed human-made molecular computers. Such systems are characterized by the fact that each computational unit, such as a domain within a dna strand, may bind to several different partners with distinct, prescribed binding strengths. Unfortunately, implementing systems of molecular computation that incorporate non-orthogonal binding is difficult, because researchers lack a robust, general-purpose method for designing molecules with this type of behavior. In this work, we describe and demonstrate a process for the rational design of dna sequences with prescribed non-orthogonal binding behavior. this process makes use of a model that represents large sets of non-orthogonal dna sequences using fixed-length binary strings, and estimates the differential binding affinity between pairs of sequences through the Hamming distance between their corresponding binary strings. the real-world applicability of this model is supported by simulations and some experimental data. We then select two previously described systems of molecular computation involving non-orthogonal interactions, and apply our sequence design process to implement them using dna strand displacement. Our simulated results on these two systems demonstrate both digital and analog computation. We hope that this work motivates the development and implementation of new computational paradigms based on non-orthogonal binding. © Joseph Don Berleant;licensed under Creative Commons License CC-BY 4.0.

关键词： dna sequences

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Graph-theoretic formalization of hybridization in dna sticker complexes

Graph-theoretic formalization of hybridization in DNA sticke...

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17th international conference on dna computing and molecular programming

作者： Brijder, Robert Gillis, Joris J. M. Van den Bussche, Jan Hasselt Univ Diepenbeek Belgium Transnat Univ Limburg Diepenbeek Belgium

ISBN: (纸本)9783642236372

Sticker complexes are a formal graph-based data model for a restricted class of dna complexes, motivated by potential applications to databases. this data model allows for a purely declarative definition of hybridization. We introduce the notion of terminating hybridization, which intuitively means that only a finite number of different products can be generated. We characterize this notion in purely graph-theoretic terms. Under a finite alphabet, each product is shown to be of polynomial size. Yet, terminating hybridization can still produce results of exponential size, in that there may be exponentially many different (nonisomorphic) finished products. We indicate a class of complexes where hybridization is guaranteed to be polynomially bounded.

关键词： dna Hybridization Graph-theory Complexity

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Probabilistic reasoning with a Bayesian dna device based on strand displacement

Probabilistic reasoning with a Bayesian DNA device based on ...

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18th international conference on dna computing and molecular programming, dna 18

作者： Sainz De Murieta, Iñaki Rodríguez-Patón, Alfonso Campus de Montegancedo s/n Boadilla del Monte Madrid 28660 Spain

ISBN: (纸本)9783642322075

We present a computing model based on the dna strand displacement technique which performs Bayesian inference. the model will take single stranded dna as input data, representing the presence or absence of a specific molecular signal (evidence). the program logic encodes the prior probability of a disease and the conditional probability of a signal given the disease playing with a set of different dna complexes and their ratios. When the input and program molecules interact, they release a different pair of single stranded dna species whose relative proportion represents the application of Bayes' Law: the conditional probability of the disease given the signal. the models presented in this paper can empower the application of probabilistic reasoning in genetic diagnosis in vitro. © 2012 Springer-Verlag.

关键词： dna

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Reactamole: Functional reactive molecular programming 27

Reactamole: Functional reactive molecular programming

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27th international conference on dna computing and molecular programming, dna 2021

作者： Klinge, Titus H. Lathrop, James I. Osera, Peter-Michael Rogers, Allison Drake University Des MoinesIA United States Iowa State University AmesIA United States Grinnell College GrinnellIA United States

ISBN: (纸本)9783959772051

Chemical reaction networks (CRNs) are an important tool for molecular programming, a field that is rapidly expanding our ability to deploy computer programs into biological systems for a variety of applications. However, CRNs are also difficult to work with due to their massively parallel nature, leading to the need for higher-level languages that allow for easier computation with CRNs. Recently, research has been conducted into a variety of higher-level languages for deterministic CRNs but modeling CRN parallelism, managing error accumulation, and finding natural CRN representations are ongoing challenges. We introduce Reactamole, a higher-level language for deterministic CRNs that utilizes the functional reactive programming (FRP) paradigm to represent CRNs as a reactive dataflow network. Reactamole equates a CRN with a functional reactive program, implementing the key primitives of the FRP paradigm directly as CRNs. the functional nature of Reactamole makes reasoning about molecular programs easier, and its strong static typing allows us to ensure that a CRN is well-formed by virtue of being well-typed. In this paper, we describe the design of Reactamole and how we use CRNs to represent the common datatypes and operations found in FRP. We also demonstrate the potential of this functional reactive approach to molecular programming by giving an extended example where a CRN is constructed using FRP to modulate and demodulate an amplitude modulated signal. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Application programs

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Modelling and Optimisation of a dna Stack Nano-Device Using Probabilistic Model Checking 28

Modelling and Optimisation of a DNA Stack Nano-Device Using ...

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28th international conference on dna computing and molecular programming, dna 2022

作者： Li, Bowen Mackenzie, Neil Shirt-Ediss, Ben Krasnogor, Natalio Zuliani, Paolo Research Group School of Computing Newcastle University Newcastle upon Tyne United Kingdom

ISBN: (纸本)9783959772532

A dna stack nano-device is a bio-computing system that can read and write molecular signals based on dna-dna hybridisation and strand displacement. In vitro implementation of the dna stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the dna stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? the results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield. © Bowen Li, Neil Mackenzie, Ben Shirt-Ediss, Natalio Krasnogor, and Paolo Zuliani.

关键词： dna

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BWM*: A Novel, Provable, Ensemble-Based Dynamic programming Algorithm for Sparse Approximations of Computational Protein Design 1

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19th Annual international conference on Research in Computational molecular Biology (RECOMB)

作者： Jou, Jonathan D. Jain, Swati Georgiev, Ivelin Donald, Bruce R. Duke Univ Dept Comp Sci Durham NC 27706 USA Duke Univ Med Ctr Dept Biochem Durham NC 27710 USA Duke Univ Computat Biol & Bioinformat Program Durham NC USA NIAID Vaccine Res Ctr NIH Bethesda MD 20892 USA

ISBN: (数字)9783319167060

ISBN: (纸本)9783319167060;9783319167053

Current dynamic programming protein design algorithms that exploit the optimal substructure induced by sparse energy functions compute only the Global Minimum Energy Conformation (GMEC). this disproportionately favors the sequence of a single, static conformation and overlooks better sequences with multiple low-energy conformations. We propose a novel, provable, dynamic programming algorithm called Branch-Width Minimization* (BWM*) to enumerate a gap-free ensemble of conformations in order of increasing energy. Given a branch-decomposition of branch-width w for an n-residue protein design with at most q discrete side-chain conformations per residue, BWM* returns the sparse GMEC in O(nw(2)q(3/2w)) time, and enumerates each additional conformation in O(n log q) time. BWM* outperforms the classical search algorithm A* in 49 of 67 protein design problems, computing the full ensemble or a close approximation up to two orders of magnitude faster. Performance of BWM* can be predicted cheaply beforehand, allowing selection of the most efficient algorithm for each design problem.

关键词： Dynamic programming

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Improved dna-sticker arithmetic: tube-encoded-carry, Logarithmic Number System and Monte-Carlo methods

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NATURAL computing 2013年第2期12卷 235-246页

作者： Arnold, Mark G. POB 605 Laramie WY 82070 USA

the sticker model of computation, implemented using robotic processing of dna, manipulates in parallel many bitstrings, called strands, that are contained in a limited number of tubes. Prior sticker arithmetic algorithms, patterned on digital-electronics, generate carry bits in the strand, either wasting bits or using a clear operation (with problematic biochemical implementation). the novel addition algorithm here does not need to record the carry. Instead, which tube holds a particular strand implicitly encodes the carry. the speed and number of tubes are half that of prior approaches. Further encoding data in the Logarithmic Number System (LNS) allows such integer operations to perform cost-effective real multiplications, divisions and roots. An example LNS Euclidian norm is more efficient than prior methods, assuming perfect operations. Unfortunately, dna-stickers are unreliable. this paper uses sticker unreliability as a source of randomness to implement Monte-Carlo (MC) arithmetic (previously fabricated in silicon at the cost of pseudo-random generators). With stickers, the randomness is free. MC engineering mimics natural systems using unreliable but redundant components. Here, MC randomness is only useful in low-order bits. Multiple re-testing of the same bit ("refinement") trades improved reliability for slower operation using more tubes. Simulations (with different sizes, probabilities and refinement) show that increasing refinement as a function of bit position allows imperfect implementations to achieve suitable MC strand-error distributions, predicting 1000x speed-mass advantage of sticker-MCLNS over conventional supercomputers.

关键词： dna arithmetic Sticker system Addition Logarithmic Number System (LNS) Monte-Carlo Arithmetic

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molecular machines from topological linkages 27

Molecular machines from topological linkages

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27th international conference on dna computing and molecular programming, dna 2021

作者： Breik, Keenan Luchsinger, Austin Soloveichik, David The University of Texas AustinTX United States

ISBN: (纸本)9783959772051

Life is built upon amazingly sophisticated molecular machines whose behavior combines mechanical and chemical action. Engineering of similarly complex nanoscale devices from first principles remains an as yet unrealized goal of bioengineering. In this paper we formalize a simple model of mechanical motion (mechanical linkages) combined with chemical bonding. the model has a natural implementation using dna with double-stranded rigid links, and single-stranded flexible joints and binding sites. Surprisingly, we show that much of the complex behavior is preserved in an idealized topological model which considers solely the graph connectivity of the linkages. We show a number of artifacts including Boolean logic, catalysts, a fueled motor, and chemo-mechanical coupling, all of which can be understood and reasoned about in the topological model. the variety of achieved behaviors supports the use of topological chemical linkages in understanding and engineering complex molecular behaviors. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Binding sites

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Russell Deaton Akira Suyama

ISBN: (数字)9783642106040

ISBN: (纸本)9783642106033

this book constitutes the thoroughly refereed post-conference proceedings of the 15th international Meeting on dna computing, dna15, held in Fayetteville, AR, USA, in June 2009. the 16 revised full papers presented were carefully selected during two rounds of reviewing and improvement from 38 submissions. the papers feature current interdisciplinary research in molecular-scale manipulation of matter - in particular, implementation of nanoscale computation and programmed assembly of materials are of interest, thus reflecting a broader scope beyond dna-based nanotechnology and computation.

关键词： theory of Computation Biochemistry, general Nanotechnology and Microengineering Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics

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COMPUTATIONAL dna DROPLETS BASED ON LIQUID-LIQUID PHASE SEPARATION FOR CANCER DIAGNOSIS 26

COMPUTATIONAL DNA DROPLETS BASED ON LIQUID-LIQUID PHASE SEPA...

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26th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2022

作者： Gong, Jing Tsumura, Nozomi Sato, Yusuke Takinoue, Masahiro Tokyo Institute of Technology Japan Kyushu Institute of Technology Japan

ISBN: (纸本)9781733419048

We demonstrate a computational dna droplet that can recognize specific combinations of tumor marker microRNAs (miRNAs) as molecular inputs and output the results of dna logic operations through physical dna droplet phase separation, which achieves the fusion of biosensing and molecular logic computation in dna droplets. Phase-separated biomolecular droplets are formed in cells to regulate various biological processes. Such droplet systems can be reproduced by programmable phase-separated droplets, called dna droplets, as artificial intracellular compartments. We integrated biosensing and logic computing into dna droplets to achieve information processing control. We demonstrated that upon reaction with miRNAs, the computational dna droplet was phase-separated into three dna droplets and can perform miRNA pattern recognition represented by the logical formula ((miRNA-1 ∧ miRNA-2) ∧ (miRNA-3 ∧ ¬miRNA-4)). © 2022 MicroTAS 2022 - 26th international conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： dna

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